SEPAS_Affinity_V1 (Jun, 2019)

Address: Hamid Hadi-Alijanvand,
Department of Biological Sciences,
Institute for Advanced Studies in Basic Sciences (IASBS),
Zanjan, 45137-66731, Iran.
P.O. Box: 45195-1159
Lab: www.biophysics.ir
Email: hhadi@iasbs.ac.ir; h2a1385@gmail.com

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System requirement:
Linux x86-64
VMD 1.9.2 (set it in PATH)

* SEPAS_Affinity_V1 provides you the predicted affinity-class of the provided protein binding patch (PBP).

Help:
The binary version of SEPAS just needs to a file that it contains the "resid" of the protein binding patch's residues and the 3D structure of one subunit in PDB format.

* SEPAS_Affinity_V1 just reads the file named by "PBP_Affinity.dat". This file contains the name of PBP file and information of about PBP. The binary run file, " PBP_Affinity.dat" and "PDB file" would be in same directory. SEPAS_ Affinity writes the output into "PredAffn **.dat" file.

<<Please do not rename the input files, let them named by "PBP_Affinity.dat">>
- Please let SEPAS to read and write via chmod (like chmod 775 permisions) command.
- Execute in shell; $ ./ SEPAS_Affinity_V1 press return


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Input format:

The format of "PBP_Affinity.dat" as the input files for SEPAS:
Column 1: The name of the 3D structure file contains the desired subunit in PDB format. The suffix of structure file should be ".pdb". Please just intoduce the file name without suffix in first column.
Column 2: It indicates the name of the desired chain that the suggested PBP resides on it.
Column 3: It lets you to add one word as extra information to the input file. For example add "X" there.
Column 4 and > 4: Please add the "resids" of the desired PBP in forth column. The "resid" follows the VMD standards.


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Output format:

A) The output file of SEPAS_Affinity_V1 which is named "PredAffn **.dat" contain following information;
Line 1-Some contact information.
Line 3-"-----" act as separators.
Line 4- Blank line
Line 5- The name of PDB file / the introduced chain ID of the desired subunit / the size of provided PBP / extra information that you provide in input file
Line 6- The predicted affinity label for the suggested PBP is provided (High/High-Medium/Low-Medium/Low). This class is predicted for the affinity of the desired subunits in solution context.
Line 7- The probability of the assigned class. If it closes to 1 it mean the prediction is more confident.
Line 8- The average affinity value of the assigned class is mentioned.
Line 9- The average degree of fold of the assigned class is mentioned.
Line 10- The predicted affinity value for the provide PBP is predicted.








 




